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- PDB-1ce4: CONFORMATIONAL MODEL FOR THE CONSENSUS V3 LOOP OF THE ENVELOPE PR... -

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Basic information

Entry
Database: PDB / ID: 1ce4
TitleCONFORMATIONAL MODEL FOR THE CONSENSUS V3 LOOP OF THE ENVELOPE PROTEIN GP120 OF HIV-1
ComponentsPROTEIN (V3 LOOP OF HIV-1 ENVELOPE PROTEIN)
KeywordsVIRAL PROTEIN / AMPHIPATHIC HELIX / HIV INFECTION
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / positive regulation of cell growth / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / positive regulation of cell growth / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
MethodSOLUTION NMR / distance geometry
AuthorsVranken, W.F. / Fant, F. / Budesinsky, M. / Borremans, F.A.M.
CitationJournal: FEBS Lett. / Year: 1995
Title: The complete Consensus V3 loop peptide of the envelope protein gp120 of HIV-1 shows pronounced helical character in solution.
Authors: Vranken, W.F. / Budesinsky, M. / Fant, F. / Boulez, K. / Borremans, F.A.
History
DepositionMar 15, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (V3 LOOP OF HIV-1 ENVELOPE PROTEIN)


Theoretical massNumber of molelcules
Total (without water)3,9051
Polymers3,9051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500LOWEST TARGET FUNCTION
RepresentativeModel #1

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Components

#1: Protein/peptide PROTEIN (V3 LOOP OF HIV-1 ENVELOPE PROTEIN)


Mass: 3905.409 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SEQUENCE TAKEN FROM HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (CLONE 12), GENE ENV
References: UniProt: P20871

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
131CT-NOESY

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Sample preparation

DetailsContents: 10% D2O/70% WATER/20% D3-TRIFLUOROETHANOL
Sample conditionspH: 2.5 / Pressure: 1 atm / Temperature: 290 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AM / Manufacturer: Bruker / Model: AM / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
DiscoverBIOSYMrefinement
UXNMRstructure solution
Prontostructure solution
DIANAstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: THE 20 STRUCTURES WITH LOWEST TARGET FUNCTION FROM DIANA WERE ENERGY MINIMIZED IN THE AMBER FORCE FIELD USING 500 ITERATIONS STEEPEST DESCENT FOLLOWED BY 500 ITERATIONS CONJUGATE GRADIENT MINIMIZATION.
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 500 / Conformers submitted total number: 20

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